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Crystal structure of N-methyl transferase from Plasmodium knowlesi complexed with S-adenosyl methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 282 Protein solution was at 15 mg/mL containing 20 mM Tris, 100 mM NaCl, 2 mM EDTA and 5 mM bME, 5 mM SAM. Mother liqueur contained 0.1 M Na-acetate (pH 5.0) and 20% PEG 3.350. Cryoprotectant was 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.71 α = 90 b = 96.76 β = 90 c = 38.46 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2012-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 20 99.8 0.089 12.81 51102 51018 -3 30.857
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.748 2.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3UJ7 1.9 19.7 51016 50979 2549 99.83 0.253 0.2347 0.2328 0.2331 0.2708 0.271 RANDOM 27.0975
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.09 0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.762 r_dihedral_angle_3_deg 13.938 r_dihedral_angle_4_deg 10.74 r_dihedral_angle_1_deg 5.082 r_angle_refined_deg 1.147 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4048 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 62
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction PHASER phasing